There's an Open Letter to
DOOM fans on HomeLAN Fed where scriptwriter explains the changes to the
DOOM story for the film adaptation, responding to concerns that what story the
game originally presented is being changed:

The screenplay I wrote DOES
differ in a number of ways from the games. I want to be very honest and
forthcoming in saying that, and I know that I won't make any friends amongst the
fans of the game in doing so. But it should be mentioned that it was never the
goal of anyone involved in this film, from myself and the producers to the
studio to the guys at id, to make a direct film adaptation of the game(s). The
thought process has always been to create an extension of the Doom universe that
will give fans an interesting new take on the themes that they've come to enjoy
in the game. Because let's be honest here: as far as a completely immersive and
cinematic experience, we were never going to top Doom 3 anyway, and we all knew
that. Instead, we have toyed with some elements of the game, and yes, I am
pretty much solely responsible for that, since it was my pitch and my screenplay
that got made. Let me assure you, though, that the themes and elements that you
love about Doom are ALL represented strongly in the film...just with some new
twists.